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    RAB3GAP1 RAB3 GTPase activating protein catalytic subunit 1 [ Homo sapiens (human) ]

    Gene ID: 22930, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RAB3GAP1provided by HGNC
    Official Full Name
    RAB3 GTPase activating protein catalytic subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:17063
    See related
    Ensembl:ENSG00000115839 MIM:602536; AllianceGenome:HGNC:17063
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    P130; MARTS2; WARBM1; RAB3GAP; RAB3GAP130
    Summary
    This gene encodes the catalytic subunit of a Rab GTPase activating protein. The encoded protein forms a heterodimer with a non-catalytic subunit to specifically regulate the activity of members of the Rab3 subfamily of small G proteins. This protein mediates the hydrolysis of GTP bound Rab3 to the GDP bound form. Mutations in this gene are associated with Warburg micro syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]
    Expression
    Ubiquitous expression in brain (RPKM 16.8), thyroid (RPKM 15.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAB3GAP1 in Genome Data Viewer
    Location:
    2q21.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135052292..135176396)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (135492756..135617244)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135809862..135928280)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135732781-135733282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135733283-135733782 Neighboring gene cyclin T2 Neighboring gene mitogen-activated protein kinase kinase kinase 19 Neighboring gene MPRA-validated peak3873 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16570 Neighboring gene small nucleolar RNA U13 Neighboring gene HNF4 motif-containing MPRA enhancer 203 Neighboring gene small nucleolar RNA, H/ACA box 40B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:135970274-135970798 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:135980911-135981075 Neighboring gene uncharacterized LOC124906077 Neighboring gene zinc finger RANBP2-type containing 3 Neighboring gene MPRA-validated peak3875 silencer Neighboring gene G3BP1 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Autosomal recessive microcephaly, microcornea, congenital cataract, mental retardation, optic atrophy, and hypogenitalism. Micro syndrome. Warburg M, et al. Am J Dis Child, 1993 Dec. PMID 8249951
    2. Revealing the functions of novel mutations in RAB3GAP1 in Martsolf and Warburg micro syndromes. Koparir A, et al. Am J Med Genet A, 2019 Apr. PMID 30730599
    3. Novel RAB3GAP1 compound heterozygous mutations in Japanese siblings with Warburg Micro syndrome. Asahina M, et al. Brain Dev, 2016 Mar. PMID 26421802
    4. Consanguinity as an Adjunct Diagnostic Tool. Srivastava P, et al. Indian J Pediatr, 2016 Mar. PMID 26138576
    5. [Analysis of a case of Warburg micro syndrome type 1 due to variant of RAB3GAP1 gene]. Yang D, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2020 Dec 10. PMID 33306828

    See all (115) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exome sequencing identifies a novel pathogenic variant in RAB3GAP1 causing Warburg Micro syndrome in a Pakistani family.
      Title: Exome sequencing identifies a novel pathogenic variant in RAB3GAP1 causing Warburg Micro syndrome in a Pakistani family.
    2. Proteasomal degradation of p130 facilitate cell cycle deregulation and impairment of cellular differentiation in high-risk Human Papillomavirus 16 and 18 E7 transfected cells.
      Title: Proteasomal degradation of p130 facilitate cell cycle deregulation and impairment of cellular differentiation in high-risk Human Papillomavirus 16 and 18 E7 transfected cells.
    3. Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
      Title: Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
    4. Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report.
      Title: Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report.
    5. [Analysis of a case of Warburg micro syndrome type 1 due to variant of RAB3GAP1 gene].
      Title: [Analysis of a case of Warburg micro syndrome type 1 due to variant of RAB3GAP1 gene].
    6. Mutations in RAB3GAP1 gene are associated with Martsolf and Warburg micro syndromes.
      Title: Revealing the functions of novel mutations in RAB3GAP1 in Martsolf and Warburg micro syndromes.
    7. overexpressing p130 or E2F4 significantly improved migration but not proliferation of mMSCs. Our data suggest that cell cycle regulation may be involved in p130/E2F4-mediated changes in the multipotential abilities of bone-marrow-derived mesenchymal stem cells (MSCs).
      Title: Stable overexpression of p130/E2F4 affects the multipotential abilities of bone-marrow-derived mesenchymal stem cells.
    8. Whole-exome sequencing, using DNA of the first fetus, was performed shortly after the birth of a male child, and two truncating RAB3GAP1 mutations were detected: c.538G>T; p. (Glu180*) and c.943C>T; p. (Arg315*).
      Title: Early detection of bilateral cataracts in utero may represent a manifestation of severe congenital disease.
    9. show that FOXC1 regulates the expression of RAB3GAP1, RAB3GAP2 and SNAP25
      Title: FOXC1 modulates MYOC secretion through regulation of the exocytic proteins RAB3GAP1, RAB3GAP2 and SNAP25.
    10. RAB18 modulates macroautophagy and proteostasis, and is dependent on activity of RAB3GAP1 and RAB3GAP2.
      Title: The RAB GTPase RAB18 modulates macroautophagy and proteostasis.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Martsolf syndrome 2
    MedGen: C5543626 OMIM: 619420 GeneReviews: Not available
    		not available
    Warburg micro syndrome 1
    MedGen: C1838625 OMIM: 600118 GeneReviews: RAB18 Deficiency
    		not available

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries.
    EBI GWAS Catalog
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0066, DKFZp434A012

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTPase activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    contributes_to guanyl-nucleotide exchange factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in camera-type eye development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in establishment of protein localization to endoplasmic reticulum membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in excitatory postsynaptic potential ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in face morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in hypothalamus development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within lipid droplet organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of endoplasmic reticulum tubular network organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein lipidation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of calcium ion-dependent exocytosis of neurotransmitter ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of short-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum tubular network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in lipid droplet IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    rab3 GTPase-activating protein catalytic subunit
    Names
    RAB3 GTPase activating protein subunit 1 (catalytic)
    RAB3 GTPase-activating protein 130 kDa subunit
    rab3-GAP p130

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016972.2 RefSeqGene

      Range
      5002..123420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172435.2 → NP_001165906.1  rab3 GTPase-activating protein catalytic subunit isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC017031, BC071602, DA333844
      Consensus CDS
      CCDS54402.1
      Related
      ENSP00000411418.1, ENST00000442034.5
      Conserved Domains (2) summary
      pfam13890
      Location:612 → 769
      Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit
      pfam15810
      Location:881 → 970
      CCDC117; Coiled-coil domain-containing protein 117

    2. NM_012233.3 → NP_036365.1  rab3 GTPase-activating protein catalytic subunit isoform 2

      See identical proteins and their annotated locations for NP_036365.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC017031, D31886, DA333844
      Consensus CDS
      CCDS33294.1
      UniProtKB/Swiss-Prot
      A6H8Z3, C9J837, Q15042, Q659F5, Q8TBB4
      UniProtKB/TrEMBL
      B9A6J2
      Related
      ENSP00000264158.8, ENST00000264158.13
      Conserved Domains (1) summary
      pfam13890
      Location:612 → 769
      Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      135052292..135176396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510823.4 → XP_011509125.1  rab3 GTPase-activating protein catalytic subunit isoform X1

      UniProtKB/TrEMBL
      A0A8J9AUI2
      Related
      ENSP00000444306.2, ENST00000539493.3
      Conserved Domains (1) summary
      pfam13890
      Location:612 → 769
      Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

    2. XM_011510825.4 → XP_011509127.1  rab3 GTPase-activating protein catalytic subunit isoform X2

      Conserved Domains (1) summary
      pfam13890
      Location:612 → 769
      Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

    3. XM_047443732.1 → XP_047299688.1  rab3 GTPase-activating protein catalytic subunit isoform X3

    RNA

    1. XR_001738674.3 RNA Sequence

      Related
      ENST00000487003.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      135492756..135617244
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341044.1 → XP_054197019.1  rab3 GTPase-activating protein catalytic subunit isoform X1

      UniProtKB/TrEMBL
      A0A8J9AUI2

    2. XM_054341045.1 → XP_054197020.1  rab3 GTPase-activating protein catalytic subunit isoform X2

    3. XM_054341046.1 → XP_054197021.1  rab3 GTPase-activating protein catalytic subunit isoform X3

    RNA

    1. XR_008486307.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15042.3 GenPept UniProtKB/Swiss-Prot:Q15042

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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